Image courtesy of N. Patel and N. Putnam, University of California, Berkeley, USA

What can the genome of a jawless worm-like marine animal tell us about vertebrate evolution? The publication in Nature of the amphioxus genome provides information on the genome duplications that have occurred in the vertebrate lineage and gives a picture of the genome of the last common ancestor of all chordates. Such information offers insights into the functional biology of various vertebrate species.

Amphioxus (also known as a lancelet) is a member of the cephalochordates, which, together with tunicates and vertebrates, make up the chordate phylum. The three groups diverged from each other about 550 million years ago, but until now the order in which they diverged has not been certain.

Putnam et al. obtained the sequence of the 520 Mb genome by shotgun sequencing from a single male amphioxus. As genetic and physical maps are not available, the sequences could not be assigned to the 19 amphioxus chromosomes; however, the assembled scaffolds were sufficiently large to provide information about synteny with other species. The genome contains 21,900 protein-coding genes, and also the highest level of polymorphism yet found in an organism whose genome has been sequenced, implying a large effective population size.

The authors used the sequences of 1,090 amphioxus genes and their orthologues in other organisms to confirm that amphioxus diverged from vertebrates and tunicates before they diverged from each other, but that the three do form a monophyletic group, contrary to some recent claims about amphioxus being the sister group of echinoderms. By studying the synteny between species, the authors could reconstruct 17 putative linkage groups for the last common ancestor of chordates. When they compared these groups between amphioxus and humans, each amphioxus group corresponded to four human groups, confirming that there have been two genome duplications during vertebrate evolution, although the majority of duplicate genes have subsequently been lost. Intriguingly, genes retained in multiple copies are enriched for developmental signalling genes and transcriiption factors, hinting at the origins of vertebrate developmental complexity.

The amphioxus sequence has also yielded insights about intron structure and the conservation of non-coding regions. A series of accompanying papers in Genome Research explores the biological insights that have derived from this genome, including for the immune system and neural development.